Normal mode analysis of G-actin

Abstract

We undertook a normal mode analysis of the G-actin monomer bound with ADP and Ca2+, in order to better understand the internal modes of this protein. The internal co-ordinates consisted of 1373 single bond torsions, plus an additional 11 torsions to parameterize the motion of the nucleotide and cation with respect to the protein. A generalized eigenvalue problem was solved to yield a complete description of the motion in the 0.1 to 17.0 picosecond time range. The modes were visualized using an interactive graphics routine. The softest, slowest modes include a propeller-like twisting of the large and small domain about the phosphate binding loops, a rolling of subdomain 4 about an alpha-helix axis and a scissor-type opening and closing of the ADP-binding cleft. The computed temperature factors agree well with experimental ones. A comparable analysis done on G-actin-ATP shows that the softest modes are almost identical.